io.github.msdk.featuredetection.adap3d.algorithms

Class CurveTool

java.lang.Object

io.github.msdk.featuredetection.adap3d.algorithms.CurveTool

public class CurveTool
extends Object

CurveTool class is used for estimation of Full width half maximum.

Field Summary

Fields

Modifier and Type	Field and Description
static double	FWHM_CONSTANT Constant FWHM_CONSTANT=2.35482

Constructor Summary

Constructors

Constructor and Description
CurveTool(SliceSparseMatrix sliceSparseMatrix) CurveTool constructor takes object of SliceSparseMatrix class.

Method Summary

Modifier and Type	Method and Description
double	estimateFwhmMs() estimateFwhmMs method estimates the FWHM for given number of random scans.
static double	normalize(double[] values, double[] normValues) normalize method is used for normalizing values by calculating its area and dividing each value by the area.
static float	normalize(float[] values) normalize.
static double	normalize(List<SliceSparseMatrix.Triplet> slice, int leftBound, int rightBound, int roundedMz, double[] referenceEIC) normalize method is used for normalizing EIC by calculating its area and dividing each intensity by the area.
static double	similarityValue(double[] referenceEIC, double[] gaussianValues, int leftBound, int rightBound) similarityValue.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

FWHM_CONSTANT

public static final double FWHM_CONSTANT

Constant FWHM_CONSTANT=2.35482

See Also:

Constant Field Values

Constructor Detail

CurveTool

public CurveTool(SliceSparseMatrix sliceSparseMatrix)

CurveTool constructor takes object of SliceSparseMatrix class.

Parameters:

sliceSparseMatrix - a SliceSparseMatrix object.

Method Detail

estimateFwhmMs

public double estimateFwhmMs()

estimateFwhmMs method estimates the FWHM for given number of random scans.

Returns:

fwhm a Double object.This is Full width half maximum.

similarityValue

public static double similarityValue(double[] referenceEIC,
                                     double[] gaussianValues,
                                     int leftBound,
                                     int rightBound)

similarityValue.

Parameters:

referenceEIC - an array of double.

gaussianValues - an array of double.

leftBound - a int.

rightBound - a int.

Returns:

a double.

normalize

public static double normalize(List<SliceSparseMatrix.Triplet> slice,
                               int leftBound,
                               int rightBound,
                               int roundedMz,
                               double[] referenceEIC)

normalize method is used for normalizing EIC by calculating its area and dividing each intensity by the area.

Parameters:

roundedMz - a Integer object.This is m/z value which is multiplied by 10000 because of it's use in sparse matrix.

leftBound - a Integer object. This is lowest scan number from which peak determining starts.

rightBound - a Integer object. This is highest scan number on which peak determining ends.

referenceEIC - a Double array. This array contains normalize intensities for given m/z value.(Intensities/area)

slice - a List object.

Returns:

area a Double object. This is area of normalize intensity points.

normalize

public static double normalize(double[] values,
                               double[] normValues)

normalize method is used for normalizing values by calculating its area and dividing each value by the area.

Parameters:

values - a Double array. This array will have values to be normalized.

normValues - a Double array. This array will have normalized values.

Returns:

area a Double object. This is area of normalize intensity points.

normalize

public static float normalize(float[] values)

normalize.

Parameters:

values - an array of float.

Returns:

a float.